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Aharon-Yariv A, Wang Y, Ahmed A, Delgado-Olguín P. Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart. BMC Genomics 2023; 24:709. [PMID: 37996818 PMCID: PMC10668469 DOI: 10.1186/s12864-023-09801-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases in a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific transcriptional programs. However, small RNA expression dynamics and genome-wide miRNA regulatory networks controlling maturation of the human fetal heart remain poorly understood. RESULTS Transcriptome profiling of small RNAs revealed the temporal expression patterns of miRNA, piRNA, circRNA, snoRNA, snRNA and tRNA in the developing human heart between 8 and 19 weeks of gestation. Our analysis demonstrated that miRNAs were the most dynamically expressed small RNA species throughout mid-gestation. Cross-referencing differentially expressed miRNAs and mRNAs predicted 6200 mRNA targets, 2134 of which were upregulated and 4066 downregulated as gestation progressed. Moreover, we found that downregulated targets of upregulated miRNAs, including hsa-let-7b, miR-1-3p, miR-133a-3p, miR-143-3p, miR-499a-5p, and miR-30a-5p predominantly control cell cycle progression. In contrast, upregulated targets of downregulated miRNAs, including hsa-miR-1276, miR-183-5p, miR-1229-3p, miR-615-3p, miR-421, miR-200b-3p and miR-18a-3p, are linked to energy sensing and oxidative metabolism. Furthermore, integrating miRNA and mRNA profiles with proteomes and reporter metabolites revealed that proteins encoded in mRNA targets and their associated metabolites mediate fatty acid oxidation and are enriched as the heart develops. CONCLUSIONS This study presents the first comprehensive analysis of the small RNAome of the maturing human fetal heart. Our findings suggest that coordinated activation and repression of miRNA expression throughout mid-gestation is essential to establish a dynamic miRNA-mRNA-protein network that decreases cardiomyocyte proliferation potential while increasing the oxidative capacity of the maturing human fetal heart. Our results provide novel insights into the molecular control of metabolic maturation of the human fetal heart.
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Affiliation(s)
- Adar Aharon-Yariv
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yaxu Wang
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Abdalla Ahmed
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Paul Delgado-Olguín
- Translational Medicine, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G0A4, Canada.
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Heart & Stroke, Richard Lewar Centre of Excellence, Toronto, Ontario, Canada.
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Klaassen S, Kühnisch J, Schultze-Berndt A, Seidel F. Left Ventricular Noncompaction in Children: The Role of Genetics, Morphology, and Function for Outcome. J Cardiovasc Dev Dis 2022; 9:jcdd9070206. [PMID: 35877568 PMCID: PMC9320003 DOI: 10.3390/jcdd9070206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/05/2023] Open
Abstract
Left ventricular noncompaction (LVNC) is a ventricular wall anomaly morphologically characterized by numerous, excessively prominent trabeculations and deep intertrabecular recesses. Accumulating data now suggest that LVNC is a distinct phenotype but must not constitute a pathological phenotype. Some individuals fulfill the morphologic criteria of LVNC and are without clinical manifestations. Most importantly, morphologic criteria for LVNC are insufficient to diagnose patients with an associated cardiomyopathy (CMP). Genetic testing has become relevant to establish a diagnosis associated with CMP, congenital heart disease, neuromuscular disease, inborn error of metabolism, or syndromic disorder. Genetic factors play a more decisive role in children than in adults and severe courses of LVNC tend to occur in childhood. We reviewed the current literature and highlight the difficulties in establishing the correct diagnosis for children with LVNC. Novel insights show that the interplay of genetics, morphology, and function determine the outcome in pediatric LVNC.
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Affiliation(s)
- Sabine Klaassen
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (J.K.); (A.S.-B.); (F.S.)
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Department of Paediatric Cardiology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- Correspondence: ; Tel.: +49-30-9406-3319; Fax: +49-30-9406-3358
| | - Jirko Kühnisch
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (J.K.); (A.S.-B.); (F.S.)
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
| | - Alina Schultze-Berndt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (J.K.); (A.S.-B.); (F.S.)
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, 13125 Berlin, Germany
- Department of Paediatric Cardiology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Franziska Seidel
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (J.K.); (A.S.-B.); (F.S.)
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Department of Paediatric Cardiology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- Department of Congenital Heart Disease-Paediatric Cardiology, German Heart Institute Berlin, 13353 Berlin, Germany
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Rojanasopondist P, Nesheiwat L, Piombo S, Porter GA, Ren M, Phoon CKL. Genetic Basis of Left Ventricular Noncompaction. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003517. [PMID: 35549379 DOI: 10.1161/circgen.121.003517] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Left ventricular noncompaction (LVNC) is the third most common pediatric cardiomyopathy characterized by a thinned myocardium and prominent trabeculations. Next-generation genetic testing has led to a rapid increase in the number of genes reported to be associated with LVNC, but we still have little understanding of its pathogenesis. We sought to grade the strength of the gene-disease relationship for all genes reported to be associated with LVNC and identify molecular pathways that could be implicated. METHODS Following a systematic PubMed review, all genes identified with LVNC were graded using a validated, semi-quantitative system based on all published genetic and experimental evidence created by the Clinical Genome Resource (ClinGen). Genetic pathway analysis identified molecular processes and pathways associated with LVNC. RESULTS We identified 189 genes associated with LVNC: 11 (6%) were classified as definitive, 21 (11%) were classified as moderate, and 140 (74%) were classified as limited, but 17 (9%) were classified as no evidence. Of the 32 genes classified as definitive or moderate, the most common gene functions were sarcomere function (n=11; 34%), transcriptional/translational regulator (n=6; 19%), mitochondrial function (n=3; 9%), and cytoskeletal protein (n=3; 9%). Furthermore, 18 (56%) genes were implicated in noncardiac syndromic presentations. Lastly, 3 genetic pathways (cardiomyocyte differentiation via BMP receptors, factors promoting cardiogenesis in vertebrates, and Notch signaling) were found to be unique to LVNC and not overlap with pathways identified in dilated cardiomyopathy and hypertrophic cardiomyopathy. CONCLUSIONS LVNC is a genetically heterogeneous cardiomyopathy. Distinct from dilated or hypertrophic cardiomyopathies, LVNC appears to arise from abnormal developmental processes.
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Affiliation(s)
- Pakdee Rojanasopondist
- Division of Pediatric Cardiology, Department of Pediatrics (P.R., L.N., S.P., C.K.L.P.), NYU Grossman School of Medicine, NY
| | - Leigh Nesheiwat
- Division of Pediatric Cardiology, Department of Pediatrics (P.R., L.N., S.P., C.K.L.P.), NYU Grossman School of Medicine, NY
| | - Sebastian Piombo
- Division of Pediatric Cardiology, Department of Pediatrics (P.R., L.N., S.P., C.K.L.P.), NYU Grossman School of Medicine, NY
| | - George A Porter
- Division of Pediatric Cardiology, Department of Pediatrics, University of Rochester School of Medicine, NY (G.A.P.)
| | - Mindong Ren
- Departments of Anesthesiology and Cell Biology (M.R.), NYU Grossman School of Medicine, NY
| | - Colin K L Phoon
- Division of Pediatric Cardiology, Department of Pediatrics (P.R., L.N., S.P., C.K.L.P.), NYU Grossman School of Medicine, NY
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Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart. Cell Rep 2020; 26:1934-1950.e5. [PMID: 30759401 DOI: 10.1016/j.celrep.2019.01.079] [Citation(s) in RCA: 271] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/14/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
The heart is the central organ of the circulatory system, and its proper development is vital for maintaining human life. Here, we used single-cell RNA sequencing to profile the gene expression landscapes of ∼4,000 cardiac cells from human embryos and identified four major types of cells: cardiomyocytes (CMs), cardiac fibroblasts, endothelial cells (ECs), and valvar interstitial cells (VICs). Atrial and ventricular CMs acquired distinct features early in heart development. Furthermore, both CMs and fibroblasts show stepwise changes in gene expression. As development proceeds, VICs may be involved in the remodeling phase, and ECs display location-specific characteristics. Finally, we compared gene expression profiles between humans and mice and identified a series of unique features of human heart development. Our study lays the groundwork for elucidating the mechanisms of in vivo human cardiac development and provides potential clues to understand cardiac regeneration.
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Lopez AL, Larina IV. Second harmonic generation microscopy of early embryonic mouse hearts. BIOMEDICAL OPTICS EXPRESS 2019; 10:2898-2908. [PMID: 31259060 PMCID: PMC6583332 DOI: 10.1364/boe.10.002898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 05/15/2023]
Abstract
The understanding of biomechanical regulation of early heart development in genetic mouse models can contribute to improved management of congenital cardiovascular defects and embryonic cardiac failures in humans. The extracellular matrix (ECM), and particularly fibrillar collagen, are central to heart biomechanics, regulating tissue strength, elasticity and contractility. Here, we explore second harmonic generation (SHG) microscopy for visualization of establishing cardiac fibers such as collagen in mouse embryos through the earliest stages of development. We detected significant increase in SHG positive fibrillar content and organization over the first 24 hours after initiation of contractions. SHG microscopy revealed regions of higher fibrillar organization in regions of higher contractility and reduced fibrillar content and organization in mouse Mlc2a model with cardiac contractility defect, suggesting regulatory role of mechanical load in production and organization of structural fibers from the earliest stages. Simultaneous volumetric SHG and two-photon excitation microscopy of vital fluorescent reporter EGFP in the heart was demonstrated. In summary, these data set SHG microscopy as a valuable non-bias imaging tool to investigate mouse embryonic cardiogenesis and biomechanics.
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Affiliation(s)
- Andrew L. Lopez
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Irina V. Larina
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Bourke L, del Monte-Nieto G, Outhwaite J, Bharti V, Pollock P, Simmons D, Adam A, Hur S, Maghzal G, Whitelaw E, Stocker R, Suter C, Harvey R, Harten S. Loss of Rearranged L-Myc Fusion (RLF) results in defects in heart development in the mouse. Differentiation 2017; 94:8-20. [DOI: 10.1016/j.diff.2016.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 01/22/2023]
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McKinnon D, Rosati B. Transmural gradients in ion channel and auxiliary subunit expression. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 122:165-186. [PMID: 27702655 DOI: 10.1016/j.pbiomolbio.2016.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/30/2016] [Indexed: 12/11/2022]
Abstract
Evolution has acted to shape the action potential in different regions of the heart in order to produce a maximally stable and efficient pump. This has been achieved by creating regional differences in ion channel expression levels within the heart as well as differences between equivalent cardiac tissues in different species. These region- and species-dependent differences in channel expression are established by regulatory evolution, evolution of the regulatory mechanisms that control channel expression levels. Ion channel auxiliary subunits are obvious targets for regulatory evolution, in order to change channel expression levels and/or modify channel function. This review focuses on the transmural gradients of ion channel expression in the heart and the role that regulation of auxiliary subunit expression plays in generating and shaping these gradients.
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Affiliation(s)
- David McKinnon
- Department of Veterans Affairs Medical Center, Northport, NY, USA; Institute of Molecular Cardiology, Stony Brook University, Stony Brook, NY, USA; Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Barbara Rosati
- Department of Veterans Affairs Medical Center, Northport, NY, USA; Institute of Molecular Cardiology, Stony Brook University, Stony Brook, NY, USA; Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, 11794, USA.
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Zhang Y, Wang H, Wen D, Zhang J, Zheng F, Jiang N, Ma D. Tissue factor pathway inhibitor-2 is critical in zebrafish cardiogenesis. Biochem Biophys Res Commun 2015; 456:827-33. [DOI: 10.1016/j.bbrc.2014.12.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 12/04/2014] [Indexed: 02/05/2023]
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Grant et al. 1926 did not provide the first description of left ventricular hypertrabeculation/noncompaction. Int J Cardiol 2013; 169:e51-2. [DOI: 10.1016/j.ijcard.2013.08.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 08/29/2013] [Indexed: 11/18/2022]
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